Installation

Getting Multistrand

Option 1: Use online version

This is the simplest way to use Multistrand 2.0 for short
simulations. It's a temporary way for you to try out
Multistrand on an interactive IPython/Jupyter notebook
server. Experiment with the Multistrand tutorials, have
fun, and explore! Remember to save your progress offline
if you wish, as storage is ephemeral.

Hairpin Transitions.
See how to define macrostates, so that the
simulation doesn't return every elementary step,
but just returns when a macrostate is entered or
exited. See how to abulate transition
frequencies between macrostates, and examine the
consequences of using loose macrostates.

Hairpin First Passage Time.
Don't look at trajectories, just tabulate how
long they took, and compute statistics. See the
effects of kinetic traps in folding, and use the
random number seed to reproduce trajectories of
interest.

Three-way Branch Migration Energies.
See how to define complexes with multiple
strands. Consider the energy of a test tube.
Plot test tube energy for a hypothetical pathway
for toehold-mediated three-way strand
displacement.

(coming soon) Hybridization First Step Mode.
Preferred method for deducing bimolecular rate
constants. Details on more efficient simulation
that skips "equilibration" between interactions.
Deduce first-order and second-order
rate constants from probability of success and time
to completion, with error bars!

(coming soon) Hybridization Comparison.
Look at two strands interacting in a tiny box.
Compare sequences that are unstructured vs have
hairpins in various locations. Compute association
and dissociation rate constants.
Compare using first passage time, transition mode,
and first step mode. See how the time to reach a
full duplex scales with concentration.